God has been, and will always be a little too clever, perhaps even for himself. He was always in the last place you would look, and this trip down to earth was no different. He knew he would be hidden from young Castiel who hunted him all around the world. Not to mention the other angels, and the few foolish humans. Right under everyone nose, he was safe even from the Holy amulet which hung around its rightful owners neck.
It was too easy to kill the Whore of Babylon, the others looking shocked as this happen. The pain in Sam's eyes hurt him; he was after all part of this human. He looked into Zachariah's eyes just as the bodies angelic half came down from the heavens. As mentioned he did sometimes even outsmart himself, but it mostly worked itself out. As much as it pained the human, God hurt also as he watched his current host completely break, only his Sammy saved him.
Then back to work as the human brothers land smack in the middle of the ancient ones ploy. They had always been a pain in his ass, calling him a baby and being pissed when his religion started to over take theirs, but really what did they expect to happen, its really useful when you don't try and kill off all your followers.